I recently downloaded Dark Times 2 and the Dark Times maps and other add ons work perfectly fine however if I play or try to play a map with the Galactic Civil War or the Clone Wars it crashes and does not work, is there something I am doing wrong? Or has something overwrote something else as I was downloading the mod.

As I said before, please clarify your issue. Where are you seeing crashes, specifically? A useful example might be "stock Coruscant, stock GCW era." You shouldn't be seeing issues like this with just the Conversion Pack 2.0 and DT2 installed, since the two are fully compatible.